ABSTRACT: While the composition of the fish community of SW Puerto Rico has been studied extensively, little information is available on the importance of different shallow-water areas (i.e. back reef systems) as juvenile habitat. We investigated the extent to which 20 selected, reef-associated fish species use mangrove and seagrass as juvenile habitat in contrast to shallow-water coral reefs. A stratified sampling procedure was applied to quantify the variability of juvenile fish densities along the mangrove–seagrass–coral reef continuum of an inshore–offshore gradient. We recorded 28758 individuals, mainly Haemulidae, Lutjanidae, Scaridae, and Acanthuridae, with juveniles accounting for 80% of total sightings. For each fish species, juveniles were distinguished according to maturation size reported in literature. Significant variations in juvenile density were evident, and the importance of mangroves and seagrass as juvenile habitat was relative and species-specific. Frequently, shallow coral reefs showed higher densities than mangroves and seagrass. Ontogenetic migrations (i.e. progressive displacement of a given fish life stage from a given habitat to another) were inferred to occur throughout the continuum. Results highlight the importance of including this continuum within coastal management using marine reserves.